Testing Association of Groups of Genes with a Clinical Variable


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Documentation for package `globaltest' version 4.6.0

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annotation.vandeVijver Some selected annotations for the breast cancer data from Rosetta Inpharmatics LLC and Netherlands Cancer Institute, to serve as example data in the globaltest package.
checkerboard Checkerboard plot for Global Test
coefficients,mlogit-method Multinomial Logistic Regression
combine Class "gt.result" for results of the function globaltest
combine,gt.result-method Class "gt.result" for results of the function globaltest
fit Class "gt.result" for results of the function globaltest
fit,gt.result-method Class "gt.result" for results of the function globaltest
fitted.values,mlogit-method Multinomial Logistic Regression
geneplot Gene Plot for Global Test
genesets Class "GOstructure" to serve as input for the function gtGO
genesets,GOstructure-method Class "GOstructure" to serve as input for the function gtGO
getFocus Multiple testing on the GO graph
globaltest Global Test
GOstructure Class "GOstructure" to serve as input for the function gtGO
GOstructure-class Class "GOstructure" to serve as input for the function gtGO
gostructure.vandeVijver A GOstructure object for the breast cancer data from Rosetta Inpharmatics LLC and Netherlands Cancer Institute, to serve as example data in the globaltest package.
gt.barplot Class "gt.barplot" for results of the functions geneplot and sampleplot
gt.barplot-class Class "gt.barplot" for results of the functions geneplot and sampleplot
gt.multtest Correct globaltest results for multiple testing
gt.result Class "gt.result" for results of the function globaltest
gt.result-class Class "gt.result" for results of the function globaltest
gtGO Multiple testing on the GO graph
hist,gt.result-method Class "gt.result" for results of the function globaltest
length,GOstructure-method Class "GOstructure" to serve as input for the function gtGO
length,gt.barplot-method Class "gt.barplot" for results of the functions geneplot and sampleplot
length,gt.result-method Class "gt.result" for results of the function globaltest
makeGOstructure Multiple testing on the GO graph
mlogit Multinomial Logistic Regression
mlogit-class Multinomial Logistic Regression
names,gt.barplot-method Class "gt.barplot" for results of the functions geneplot and sampleplot
names,gt.result-method Class "gt.result" for results of the function globaltest
names<-,gt.barplot-method Class "gt.barplot" for results of the functions geneplot and sampleplot
names<-,gt.result-method Class "gt.result" for results of the function globaltest
p.value Class "gt.result" for results of the function globaltest
p.value,gt.result-method Class "gt.result" for results of the function globaltest
permutations Permutations version of the Global Test
plot,gt.barplot-method Class "gt.barplot" for results of the functions geneplot and sampleplot
regressionplot Regression Plot for Global Test
residuals,mlogit-method Multinomial Logistic Regression
result Class "gt.result" for results of the function globaltest
result,gt.barplot-method Class "gt.barplot" for results of the functions geneplot and sampleplot
result,gt.result-method Class "gt.result" for results of the function globaltest
sampleplot Sample Plot for Global Test
sampling Sampling random 'pathways' for the Global Test
scale,gt.barplot-method Class "gt.barplot" for results of the functions geneplot and sampleplot
show,GOstructure-method Class "GOstructure" to serve as input for the function gtGO
show,gt.barplot-method Class "gt.barplot" for results of the functions geneplot and sampleplot
show,gt.result-method Class "gt.result" for results of the function globaltest
show,mlogit-method Multinomial Logistic Regression
size Class "gt.result" for results of the function globaltest
size,gt.result-method Class "gt.result" for results of the function globaltest
sort,gt.barplot-method Class "gt.barplot" for results of the functions geneplot and sampleplot
sort,gt.result-method Class "gt.result" for results of the function globaltest
summary,mlogit-method Multinomial Logistic Regression
vandeVijver A subset of the Breast cancer data from Rosetta Inpharmatics LLC and Netherlands Cancer Institute.
z.score Class "gt.barplot" for results of the functions geneplot and sampleplot
z.score,gt.barplot-method Class "gt.barplot" for results of the functions geneplot and sampleplot
z.score,gt.result-method Class "gt.result" for results of the function globaltest
[,gt.barplot-method Class "gt.barplot" for results of the functions geneplot and sampleplot
[,gt.result-method Class "gt.result" for results of the function globaltest